Merge branch 'es5.4' of https://github.com/JULIELab/trec-pm into es5.4

JULIELab · Aug 5, 2019 · cb7750a · cb7750a
2 parents 595a4e5 + 33ced70
commit cb7750a
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Showing 3 changed files with 35 additions and 1 deletion.
diff --git a/src/main/java/at/medunigraz/imi/bst/trec/LiteratureArticlesExperimenter.java b/src/main/java/at/medunigraz/imi/bst/trec/LiteratureArticlesExperimenter.java
@@ -26,6 +26,9 @@ public static void main(String[] args) throws IOException {
         final Experiment jlpmcommon = new Experiment(GOLD_STANDARD,
                 LiteratureArticlesRetrievalRegistry.jlpmcommon(TrecConfig.SIZE));
 
+        final Experiment jlpmcommon2 = new Experiment(GOLD_STANDARD,
+                LiteratureArticlesRetrievalRegistry.jlpmcommon2(TrecConfig.SIZE));
+
         final Experiment jlpmletor = new Experiment(GOLD_STANDARD,
                 LiteratureArticlesRetrievalRegistry.jlpmletor(TrecConfig.SIZE));
         jlpmletor.setReRanker(new RankerFromPm1718());
@@ -42,7 +45,7 @@ public static void main(String[] args) throws IOException {
                 LiteratureArticlesRetrievalRegistry.jlpmtrboost(TrecConfig.SIZE));
         jlpmtrboost.setReRanker(new TreatmentRanker());
 
-        Set<Experiment> experiments = new LinkedHashSet<>(Arrays.asList(jlpmcommon, jlpmletor,jlpmltrin, jlpmtrcommon, jlpmtrboost));
+        Set<Experiment> experiments = new LinkedHashSet<>(Arrays.asList(jlpmcommon, jlpmcommon2, jlpmletor,jlpmltrin, jlpmtrcommon, jlpmtrboost));
         for (Experiment exp : experiments) {
             exp.run();
         }

diff --git a/...a/at/medunigraz/imi/bst/trec/experiment/registry/LiteratureArticlesRetrievalRegistry.java b/...a/at/medunigraz/imi/bst/trec/experiment/registry/LiteratureArticlesRetrievalRegistry.java
@@ -22,6 +22,8 @@ public final class LiteratureArticlesRetrievalRegistry {
             LiteratureArticlesRetrievalRegistry.class.getResource("/templates/biomedical_articles/boost.json").getFile());
     private static final File JULIE_COMMON_TEMPLATE = new File(
             LiteratureArticlesRetrievalRegistry.class.getResource("/templates/biomedical_articles/jlpmcommon.json").getFile());
+    private static final File JULIE_COMMON2_TEMPLATE = new File(
+            LiteratureArticlesRetrievalRegistry.class.getResource("/templates/biomedical_articles/jlpmcommon2.json").getFile());
     private static final File JULIE_BOOST_TEMPLATE = new File(
             LiteratureArticlesRetrievalRegistry.class.getResource("/templates/biomedical_articles/jlpmboost.json").getFile());
     private static final File SYNONYMS = new File(
@@ -74,6 +76,14 @@ public static TrecPmRetrieval jlpmcommon(int size) {
                 .withConditionalCancer();
     }
 
+    public static TrecPmRetrieval jlpmcommon2(int size) {
+        return new TrecPmRetrieval(TrecConfig.ELASTIC_BA_INDEX, size).withExperimentName("jlpmcommon")
+                .withSubTemplate(JULIE_COMMON2_TEMPLATE)
+                .withWordRemoval().withGeneSynonym()
+                .withDiseasePreferredTerm().withDiseaseSynonym().withSynonymList(SYNONYMS)
+                .withConditionalCancer();
+    }
+
     public static TrecPmRetrieval jlpmletor(int size) {
         return new TrecPmRetrieval(TrecConfig.ELASTIC_BA_INDEX, size).withExperimentName("jlpmletor")
                 .withSubTemplate(JULIE_COMMON_TEMPLATE)

diff --git a/src/main/resources/templates/biomedical_articles/jlpmcommon2.json b/src/main/resources/templates/biomedical_articles/jlpmcommon2.json
@@ -0,0 +1,21 @@
+{
+	"bool": {
+		"must": [
+			{{biomedical_articles/disease.json}},
+			{{biomedical_articles/gene.json}}
+		],
+		"should": [
+			{{biomedical_articles/extra.json}},
+			{{chemotherapyBoosters:biomedical_articles/conditional_chemotherapy.json}},
+			{{cancerBoosters:biomedical_articles/conditional_cancer.json}},
+			{{biomedical_articles/dna.json}},
+			{{biomedical_articles/positive_boosters.json}},
+			{{biomedical_articles/negative_boosters.json}},
+			{{biomedical_articles/exists_abstract.json}},
+			{{biomedical_articles/exists_filtered_treatment.json}}
+		],
+		"must_not": [
+			{{biomedical_articles/non_melanoma.json}}
+		]
+	}
+}